Package: clst

Version: 1.26.0

Command: /home/biocbuild/bbs-3.6-bioc/R/bin/R CMD check --no-vignettes --timings clst_1.26.0.tar.gz

StartedAt: 2018-04-11 22:19:29 -0400 (Wed, 11 Apr 2018)

EndedAt: 2018-04-11 22:20:02 -0400 (Wed, 11 Apr 2018)

EllapsedTime: 32.4 seconds

RetCode: 0

Status:  WARNINGS

CheckDir: clst.Rcheck

Warnings: 1

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###
### Running command:
###
###   /home/biocbuild/bbs-3.6-bioc/R/bin/R CMD check --no-vignettes --timings clst_1.26.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.6-bioc/meat/clst.Rcheck’
* using R version 3.4.4 (2018-03-15)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘clst/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘clst’ version ‘1.26.0’
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘clst’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... NOTE
Foreign function call to a different package:
  .C("ROC", ..., PACKAGE = "ROC")
See chapter ‘System and foreign language interfaces’ in the ‘Writing R
Extensions’ manual.
* checking R code for possible problems ... NOTE
findPMMI: no visible binding for global variable ‘median’
findPMMI: no visible global function definition for ‘quantile’
getTally: no visible binding for global variable ‘median’
scaleDistPlot: no visible global function definition for ‘cmdscale’
simpleROC: no visible global function definition for ‘new’
template: no visible global function definition for ‘str’
Undefined global functions or variables:
  cmdscale median new quantile str
Consider adding
  importFrom("methods", "new")
  importFrom("stats", "cmdscale", "median", "quantile")
  importFrom("utils", "str")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking line endings in Makefiles ... OK
* checking for GNU extensions in Makefiles ... WARNING
Found the following file(s) containing GNU extensions:
  tests/unit/Makefile
Portable Makefiles do not use GNU extensions such as +=, :=, $(shell),
$(wildcard), ifeq ... endif. See section ‘Writing portable packages’ in
the ‘Writing R Extensions’ manual.
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
               user system elapsed
scaleDistPlot 5.692   0.02   5.714
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘runalltests.R’
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 1 WARNING, 2 NOTEs
See
  ‘/home/biocbuild/bbs-3.6-bioc/meat/clst.Rcheck/00check.log’
for details.

* installing *source* package ‘clst’ ...
** R
** data
*** moving datasets to lazyload DB
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (clst)

R version 3.4.4 (2018-03-15) -- "Someone to Lean On"
Copyright (C) 2018 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library("RUnit")
> 
> options(warn=1)
> 
> dirs <- 'unit'
> 
> testFilePat <- ".*_test\\.R$"
> 
> allSuite <- defineTestSuite(name="allSuite",
+                             dirs=dirs,
+                             testFileRegexp=testFilePat,
+                             rngKind="default",
+                             rngNormalKind="default"
+                             )
> 
> testData <- runTestSuite(allSuite)


Executing test function test_strep01  ... 
   classifier (depth 1): 149 elements in reference set
   classifier (depth 1): running findThreshold, method="mutinfo"
   findThreshold (depth 1): (in): method = mutinfo
   findThreshold (depth 1): (in): within: 463   between: 10563
   findThreshold (depth 1): (out): D = 1.17 pmmi = 0.20
   classifier (depth 1): bkpt = 1.175
   classifier (depth 1): matches include S mitis, S pneumoniae, S pseudopneumoniae
 done successfully.



Executing test function test_strep02  ... 
   classifier (depth 1): 149 elements in reference set
   classifier (depth 1): running findThreshold, method="mutinfo"
   findThreshold (depth 1): (in): method = mutinfo
   findThreshold (depth 1): (in): within: 463   between: 10563
   findThreshold (depth 1): (out): D = 1.17 pmmi = 0.20
   classifier (depth 1): bkpt = 1.175
   classifier (depth 1): matches include S mitis, S pneumoniae, S pseudopneumoniae
 done successfully.



Executing test function test_strep03  ... 
   classifier (depth 1): 149 elements in reference set
   classifier (depth 1): running findThreshold, method="mutinfo"
   findThreshold (depth 1): (in): method = mutinfo
   findThreshold (depth 1): (in): within: 471   between: 10555
   findThreshold (depth 1): (out): D = 1.18 pmmi = 0.20
   classifier (depth 1): bkpt = 1.181
   classifier (depth 1): matches include S iniae
 done successfully.



Executing test function test_bvseqs01  ... 
findLowestRank: all defined ranks: superkingdom, superphylum, phylum, class, subclass, order, suborder, family, genus, species_group, species_subgroup, species
findLowestRank: lowest defined rank: 12 (species)
classifyIter: starting rank is species
   classifyIter (depth 1): 425 reference objects in 93 starting groups [470, 471, 575, 562, 838_2, 28127, 838_3, 838_4, 838_7, 28125, 838_1, 28130, 838_6, 820, 28123, 2098, 2130, 134821, 1624, 1249, 1582, 47715, 1254, 97478, 1613, 1633, 181675, 1596, 147802, 109790, 47770, 1587, 1318, 1338, 1328, 1311, 1335, 1309, 1304, 1305, 1303, 28037, 1351, 1352, 33945, 87541, 1377, 1280, 29388, 1282, 1290, 1283, 1292, 186802_1, 187101, 40543, 849, 851, 186802_2, 186802_3, 39948_2, 39948_1, 906_2, 906_1, 1261, 33037, 33036, 33033, 1260, 33030, 33031, 38284, 103621, 184870, 2052, 2051, 2702, 1685, 216816, 1681, 419015, 82135, 1383, 358, 294, 303, 47885, 47880, 70775, 76759, 78327, 316, 287]
   classify   (depth 1):
   classifier (depth 1): 425 elements in reference set
   classifier (depth 1): running findThreshold, method="mutinfo"
   findThreshold (depth 1): (in): method = mutinfo
   findThreshold (depth 1): (in): within: 797   between: 89303
   findThreshold (depth 1): (out): D = 0.09 pmmi = 0.05
   classifier (depth 1): bkpt = 0.090
   classifier (depth 1): matches include 
   classify   (depth 1): threshIsValid: TRUE 
   classify   (depth 1): moreThanOneMatch: FALSE 
   classify   (depth 1): remainingGroupsLargeEnough: FALSE 
   classify   (depth 1): remainingNotAllMatches: TRUE 
   classify   (depth 1): stopping at depth 1
   classifyIter (depth 1): no matches - redefining groups at rank 11 (species_subgroup)
      classifyIter (depth 2): 5 reference objects in 1 starting groups [578833]
      classifyIter (depth 2): only one group met screening criteria - setting dStart to 0.0888
   classify   (depth 1):
   classifier (depth 1): 5 elements in reference set
   classifier (depth 1): setting D to dStart=0.089
   classifier (depth 1): bkpt = 0.089
   classifier (depth 1): matches include 
   classify   (depth 1): threshIsValid: TRUE 
   classify   (depth 1): moreThanOneMatch: FALSE 
   classify   (depth 1): remainingGroupsLargeEnough: FALSE 
   classify   (depth 1): remainingNotAllMatches: TRUE 
   classify   (depth 1): stopping at depth 1
      classifyIter (depth 2): no matches - redefining groups at rank 10 (species_group)
         classifyIter (depth 3): 60 reference objects in 6 starting groups [655183, 671232, 136843, 136845, 136846, 136841]
   classify   (depth 1):
   classifier (depth 1): 60 elements in reference set
   classifier (depth 1): running findThreshold, method="mutinfo"
   findThreshold (depth 1): (in): method = mutinfo
   findThreshold (depth 1): (in): within: 520   between: 1250
   findThreshold (depth 1): (out): D = 0.29 pmmi = 0.29
   classifier (depth 1): bkpt = 0.286
   classifier (depth 1): matches include 
   classify   (depth 1): threshIsValid: TRUE 
   classify   (depth 1): moreThanOneMatch: FALSE 
   classify   (depth 1): remainingGroupsLargeEnough: FALSE 
   classify   (depth 1): remainingNotAllMatches: TRUE 
   classify   (depth 1): stopping at depth 1
         classifyIter (depth 3): no matches - redefining groups at rank 9 (genus)
            classifyIter (depth 4): 422 reference objects in 35 starting groups [469, 160674, 561, 838, 816, 836, 2093, 2129, 1578, 46255, 1253, 1301, 1350, 1375, 1279, 1378, 168808, 848, 39948, 906, 1257, 165779, 150022, 162289, 1716, 1654, 184869, 2050, 2701, 1678, 419014, 84111, 1380, 357, 286]
   classify   (depth 1):
   classifier (depth 1): 422 elements in reference set
   classifier (depth 1): running findThreshold, method="mutinfo"
   findThreshold (depth 1): (in): method = mutinfo
   findThreshold (depth 1): (in): within: 5585   between: 83246
   findThreshold (depth 1): (out): D = 0.51 pmmi = 0.22
   classifier (depth 1): bkpt = 0.510
   classifier (depth 1): matches include 286, 469
   classify   (depth 1): threshIsValid: TRUE 
   classify   (depth 1): moreThanOneMatch: TRUE 
   classify   (depth 1): remainingGroupsLargeEnough: TRUE 
   classify   (depth 1): remainingNotAllMatches: TRUE 
   classify   (depth 1): running classify from depth 1
      classify   (depth 2):
      classifier (depth 2): 54 elements in reference set
      classifier (depth 2): running findThreshold, method="mutinfo"
      findThreshold (depth 2): (in): method = mutinfo
      findThreshold (depth 2): (in): within: 1026   between: 405
      findThreshold (depth 2): (out): D = 0.33 pmmi = 0.85
      classifier (depth 2): bkpt = 0.330
      classifier (depth 2): matches include 469
      classify   (depth 2): threshIsValid: TRUE 
      classify   (depth 2): moreThanOneMatch: FALSE 
      classify   (depth 2): remainingGroupsLargeEnough: TRUE 
      classify   (depth 2): remainingNotAllMatches: TRUE 
      classify   (depth 2): stopping at depth 2
            classifyIter (depth 4): matchCount = 1 --> breaking

============================================================
 matches: 469
============================================================

--------------- rank species (depth 1) --------------------
thresh: prob = 0.5
classifer: minScore = 0.45  doffset = 0.5 dStart = NA
method = mutinfo  D = 0.09 pmmi = 0.049 
matches: 
      below above score match  min median  max
470       2     2  0.44     0 0.04   0.07 0.10
471       1     4  0.18     0 0.09   0.12 0.16
294       0     5  0.00     0 0.42   0.47 0.51
303       0     5  0.00     0 0.45   0.47 0.54
47880     0     5  0.00     0 0.46   0.47 0.50
70775     0     5  0.00     0 0.46   0.47 0.50
76759     0     5  0.00     0 0.45   0.48 0.51
78327     0     5  0.00     0 0.46   0.48 0.54
(... plus 85 groups not shown)

--------------- rank species_subgroup (depth 1) --------------------
thresh: prob = 
classifer: minScore = 0.45  doffset = 0.5 dStart = 0.09
method = user  D = 0.09 pmmi =  
matches: 
       below above score match min median  max
578833     0     5     0     0 0.5   0.52 0.54

--------------- rank species_group (depth 1) --------------------
thresh: prob = 0.5
classifer: minScore = 0.45  doffset = 0.5 dStart = NA
method = mutinfo  D = 0.29 pmmi = 0.287 
matches: 
       below above score match  min median  max
136843     0     5     0     0 0.42   0.47 0.51
136845     0    30     0     0 0.45   0.48 0.62
136846     0     5     0     0 0.50   0.52 0.54
136841     0     5     0     0 0.57   0.59 0.62
655183     0     5     0     0 1.50   1.51 1.51
671232     0    10     0     0 1.62   1.66 1.71

--------------- rank genus (depth 2) --------------------
thresh: prob = 0.5
classifer: minScore = 0.45  doffset = 0.5 dStart = NA
method = mutinfo  D = 0.33 pmmi = 0.845 
matches: 469
    below above score match  min median  max
469     9     0  0.95     1 0.04    0.1 0.16
286     0    45  0.00     0 0.42    0.5 0.62
----------------------------------------------

============================================================
 matches: Acinetobacter
============================================================

--------------- rank species (depth 1) --------------------
thresh: prob = 0.5
classifer: minScore = 0.45  doffset = 0.5 dStart = NA
method = mutinfo  D = 0.09 pmmi = 0.049 
matches: 
                            below above score match  min median  max
Acinetobacter baumannii         2     2  0.44     0 0.04   0.07 0.10
Acinetobacter calcoaceticus     1     4  0.18     0 0.09   0.12 0.16
Pseudomonas fluorescens         0     5  0.00     0 0.42   0.47 0.51
Pseudomonas putida              0     5  0.00     0 0.45   0.47 0.54
Pseudomonas fulva               0     5  0.00     0 0.46   0.47 0.50
Pseudomonas plecoglossicida     0     5  0.00     0 0.46   0.47 0.50
Pseudomonas monteilii           0     5  0.00     0 0.45   0.48 0.51
Pseudomonas mosselii            0     5  0.00     0 0.46   0.48 0.54
(... plus 85 groups not shown)

--------------- rank species_subgroup (depth 1) --------------------
thresh: prob = 
classifer: minScore = 0.45  doffset = 0.5 dStart = 0.09
method = user  D = 0.09 pmmi =  
matches: 
                              below above score match min median  max
Pseudomonas stutzeri subgroup     0     5     0     0 0.5   0.52 0.54

--------------- rank species_group (depth 1) --------------------
thresh: prob = 0.5
classifer: minScore = 0.45  doffset = 0.5 dStart = NA
method = mutinfo  D = 0.29 pmmi = 0.287 
matches: 
                              below above score match  min median  max
Pseudomonas fluorescens group     0     5     0     0 0.42   0.47 0.51
Pseudomonas putida group          0    30     0     0 0.45   0.48 0.62
Pseudomonas stutzeri group        0     5     0     0 0.50   0.52 0.54
Pseudomonas aeruginosa group      0     5     0     0 0.57   0.59 0.62
Lactobacillus casei group         0     5     0     0 1.50   1.51 1.51
Streptococcus anginosus group     0    10     0     0 1.62   1.66 1.71

--------------- rank genus (depth 2) --------------------
thresh: prob = 0.5
classifer: minScore = 0.45  doffset = 0.5 dStart = NA
method = mutinfo  D = 0.33 pmmi = 0.845 
matches: Acinetobacter
              below above score match  min median  max
Acinetobacter     9     0  0.95     1 0.04    0.1 0.16
Pseudomonas       0    45  0.00     0 0.42    0.5 0.62
----------------------------------------------
[1] "unit_output/test_bvseqs01.pdf"
Timing stopped at: 0.876 0.012 0.888
Error in xyplot(x ˜ y, data = data.frame(x = 1:10, y = 1:10)) : 
  could not find function "xyplot"
 done successfully.



Executing test function test_bvseqs02  ... 
   findThreshold (depth 1): (in): method = mutinfo
   findThreshold (depth 1): (in): within: 5594   between: 83659
   findThreshold (depth 1): (out): D = 0.51 pmmi = 0.22
findLowestRank: all defined ranks: superkingdom, superphylum, phylum, class, subclass, order, suborder, family, genus, species_group, species_subgroup, species
findLowestRank: lowest defined rank: 12 (species)
classifyIter: starting rank is species
   classifyIter (depth 1): 425 reference objects in 93 starting groups [470, 471, 575, 562, 838_2, 28127, 838_3, 838_4, 838_7, 28125, 838_1, 28130, 838_6, 820, 28123, 2098, 2130, 134821, 1624, 1249, 1582, 47715, 1254, 97478, 1613, 1633, 181675, 1596, 147802, 109790, 47770, 1587, 1318, 1338, 1328, 1311, 1335, 1309, 1304, 1305, 1303, 28037, 1351, 1352, 33945, 87541, 1377, 1280, 29388, 1282, 1290, 1283, 1292, 186802_1, 187101, 40543, 849, 851, 186802_2, 186802_3, 39948_2, 39948_1, 906_2, 906_1, 1261, 33037, 33036, 33033, 1260, 33030, 33031, 38284, 103621, 184870, 2052, 2051, 2702, 1685, 216816, 1681, 419015, 82135, 1383, 358, 294, 303, 47885, 47880, 70775, 76759, 78327, 316, 287]
   classify   (depth 1):
   classifier (depth 1): 425 elements in reference set
   classifier (depth 1): setting D to dStart=0.510
   classifier (depth 1): bkpt = 0.510
   classifier (depth 1): matches include 294, 303, 470, 471, 47880, 70775, 78327
   classify   (depth 1): threshIsValid: TRUE 
   classify   (depth 1): moreThanOneMatch: TRUE 
   classify   (depth 1): remainingGroupsLargeEnough: TRUE 
   classify   (depth 1): remainingNotAllMatches: TRUE 
   classify   (depth 1): running classify from depth 1
      classify   (depth 2):
      classifier (depth 2): 34 elements in reference set
      classifier (depth 2): running findThreshold, method="mutinfo"
      findThreshold (depth 2): (in): method = mutinfo
      findThreshold (depth 2): (in): within: 66   between: 495
      findThreshold (depth 2): (out): D = 0.12 pmmi = 0.09
      classifier (depth 2): bkpt = 0.121
      classifier (depth 2): matches include 470
      classify   (depth 2): threshIsValid: TRUE 
      classify   (depth 2): moreThanOneMatch: FALSE 
      classify   (depth 2): remainingGroupsLargeEnough: TRUE 
      classify   (depth 2): remainingNotAllMatches: TRUE 
      classify   (depth 2): stopping at depth 2
   classifyIter (depth 1): matchCount = 1 --> breaking

============================================================
 matches: 470
============================================================

--------------- rank species (depth 2) --------------------
thresh: prob = 0.5
classifer: minScore = 0.65  doffset = 0.5 dStart = NA
method = mutinfo  D = 0.12 pmmi = 0.092 
matches: 470
      below above score match  min median  max
470       4     0  0.89     1 0.04   0.07 0.10
471       3     2  0.55     0 0.09   0.12 0.16
294       0     5  0.00     0 0.42   0.47 0.51
303       0     5  0.00     0 0.45   0.47 0.54
47880     0     5  0.00     0 0.46   0.47 0.50
70775     0     5  0.00     0 0.46   0.47 0.50
78327     0     5  0.00     0 0.46   0.48 0.54
----------------------------------------------

============================================================
 matches: Acinetobacter baumannii
============================================================

--------------- rank species (depth 2) --------------------
thresh: prob = 0.5
classifer: minScore = 0.65  doffset = 0.5 dStart = NA
method = mutinfo  D = 0.12 pmmi = 0.092 
matches: Acinetobacter baumannii
                            below above score match  min median  max
Acinetobacter baumannii         4     0  0.89     1 0.04   0.07 0.10
Acinetobacter calcoaceticus     3     2  0.55     0 0.09   0.12 0.16
Pseudomonas fluorescens         0     5  0.00     0 0.42   0.47 0.51
Pseudomonas putida              0     5  0.00     0 0.45   0.47 0.54
Pseudomonas fulva               0     5  0.00     0 0.46   0.47 0.50
Pseudomonas plecoglossicida     0     5  0.00     0 0.46   0.47 0.50
Pseudomonas mosselii            0     5  0.00     0 0.46   0.48 0.54
----------------------------------------------
[1] "unit_output/test_bvseqs02.pdf"
 done successfully.



Executing test function test_bvseqs03  ... 
   findThreshold (depth 1): (in): method = mutinfo
   findThreshold (depth 1): (in): within: 6691   between: 82985
   findThreshold (depth 1): (out): D = 0.48 pmmi = 0.24
findLowestRank: all defined ranks: superkingdom, superphylum, phylum, class, subclass, order, suborder, family, genus, species_group, species_subgroup, species
findLowestRank: lowest defined rank: 12 (species)
classifyIter: starting rank is species
   classifyIter (depth 1): 425 reference objects in 93 starting groups [470, 471, 575, 562, 838_2, 28127, 838_3, 838_4, 838_7, 28125, 838_1, 28130, 838_6, 820, 28123, 2098, 2130, 134821, 1624, 1249, 1582, 47715, 1254, 97478, 1613, 1633, 181675, 1596, 147802, 109790, 47770, 1587, 1318, 1338, 1328, 1311, 1335, 1309, 1304, 1305, 1303, 28037, 1351, 1352, 33945, 87541, 1377, 1280, 29388, 1282, 1290, 1283, 1292, 186802_1, 187101, 40543, 849, 851, 186802_2, 186802_3, 39948_2, 39948_1, 906_2, 906_1, 1261, 33037, 33036, 33033, 1260, 33030, 33031, 38284, 103621, 184870, 2052, 2051, 2702, 1685, 216816, 1681, 419015, 82135, 1383, 358, 294, 303, 47885, 47880, 70775, 76759, 78327, 316, 287]
   classify   (depth 1):
   classifier (depth 1): 425 elements in reference set
   classifier (depth 1): setting D to dStart=0.480
   classifier (depth 1): bkpt = 0.480
   classifier (depth 1): matches include 294, 303, 470, 471, 47880, 70775
   classify   (depth 1): threshIsValid: TRUE 
   classify   (depth 1): moreThanOneMatch: TRUE 
   classify   (depth 1): remainingGroupsLargeEnough: TRUE 
   classify   (depth 1): remainingNotAllMatches: TRUE 
   classify   (depth 1): running classify from depth 1
      classify   (depth 2):
      classifier (depth 2): 29 elements in reference set
      classifier (depth 2): running findThreshold, method="mutinfo"
      findThreshold (depth 2): (in): method = mutinfo
      findThreshold (depth 2): (in): within: 56   between: 350
      findThreshold (depth 2): (out): D = 0.21 pmmi = 0.12
      classifier (depth 2): bkpt = 0.210
      classifier (depth 2): matches include 470, 471
      classify   (depth 2): threshIsValid: TRUE 
      classify   (depth 2): moreThanOneMatch: TRUE 
      classify   (depth 2): remainingGroupsLargeEnough: TRUE 
      classify   (depth 2): remainingNotAllMatches: TRUE 
      classify   (depth 2): running classify from depth 2
         classify   (depth 3):
         classifier (depth 3): 9 elements in reference set
         classifier (depth 3): running findThreshold, method="mutinfo"
         findThreshold (depth 3): (in): method = mutinfo
         findThreshold (depth 3): (in): within: 16   between: 20
         findThreshold (depth 3): (out): D = NA pmmi = -0.04
         classifier (depth 3): bkpt = NA
         classifier (depth 3): matches include 
         classify   (depth 3): threshIsValid: FALSE 
         classify   (depth 3): moreThanOneMatch: FALSE 
         classify   (depth 3): remainingGroupsLargeEnough: FALSE 
         classify   (depth 3): remainingNotAllMatches: TRUE 
         classify   (depth 3): stopping at depth 3
         classify   (depth 3): no matches on final iteration, returning previous result
   classifyIter (depth 1): no matches - redefining groups at rank 11 (species_subgroup)
      classifyIter (depth 2): 5 reference objects in 1 starting groups [578833]
      classifyIter (depth 2): only one group met screening criteria - setting dStart to 0.0888
   classify   (depth 1):
   classifier (depth 1): 5 elements in reference set
   classifier (depth 1): setting D to dStart=0.089
   classifier (depth 1): bkpt = 0.089
   classifier (depth 1): matches include 
   classify   (depth 1): threshIsValid: TRUE 
   classify   (depth 1): moreThanOneMatch: FALSE 
   classify   (depth 1): remainingGroupsLargeEnough: FALSE 
   classify   (depth 1): remainingNotAllMatches: TRUE 
   classify   (depth 1): stopping at depth 1
      classifyIter (depth 2): no matches - redefining groups at rank 10 (species_group)
         classifyIter (depth 3): 60 reference objects in 6 starting groups [655183, 671232, 136843, 136845, 136846, 136841]
   classify   (depth 1):
   classifier (depth 1): 60 elements in reference set
   classifier (depth 1): running findThreshold, method="mutinfo"
   findThreshold (depth 1): (in): method = mutinfo
   findThreshold (depth 1): (in): within: 520   between: 1250
   findThreshold (depth 1): (out): D = 0.29 pmmi = 0.29
   classifier (depth 1): bkpt = 0.286
   classifier (depth 1): matches include 
   classify   (depth 1): threshIsValid: TRUE 
   classify   (depth 1): moreThanOneMatch: FALSE 
   classify   (depth 1): remainingGroupsLargeEnough: FALSE 
   classify   (depth 1): remainingNotAllMatches: TRUE 
   classify   (depth 1): stopping at depth 1
         classifyIter (depth 3): no matches - redefining groups at rank 9 (genus)
            classifyIter (depth 4): 422 reference objects in 35 starting groups [469, 160674, 561, 838, 816, 836, 2093, 2129, 1578, 46255, 1253, 1301, 1350, 1375, 1279, 1378, 168808, 848, 39948, 906, 1257, 165779, 150022, 162289, 1716, 1654, 184869, 2050, 2701, 1678, 419014, 84111, 1380, 357, 286]
   classify   (depth 1):
   classifier (depth 1): 422 elements in reference set
   classifier (depth 1): running findThreshold, method="mutinfo"
   findThreshold (depth 1): (in): method = mutinfo
   findThreshold (depth 1): (in): within: 5585   between: 83246
   findThreshold (depth 1): (out): D = 0.51 pmmi = 0.22
   classifier (depth 1): bkpt = 0.510
   classifier (depth 1): matches include 286, 469
   classify   (depth 1): threshIsValid: TRUE 
   classify   (depth 1): moreThanOneMatch: TRUE 
   classify   (depth 1): remainingGroupsLargeEnough: TRUE 
   classify   (depth 1): remainingNotAllMatches: TRUE 
   classify   (depth 1): running classify from depth 1
      classify   (depth 2):
      classifier (depth 2): 54 elements in reference set
      classifier (depth 2): running findThreshold, method="mutinfo"
      findThreshold (depth 2): (in): method = mutinfo
      findThreshold (depth 2): (in): within: 1026   between: 405
      findThreshold (depth 2): (out): D = 0.33 pmmi = 0.85
      classifier (depth 2): bkpt = 0.330
      classifier (depth 2): matches include 469
      classify   (depth 2): threshIsValid: TRUE 
      classify   (depth 2): moreThanOneMatch: FALSE 
      classify   (depth 2): remainingGroupsLargeEnough: TRUE 
      classify   (depth 2): remainingNotAllMatches: TRUE 
      classify   (depth 2): stopping at depth 2
            classifyIter (depth 4): matchCount = 1 --> breaking

============================================================
 matches: 469
============================================================

--------------- rank species (depth 2) --------------------
thresh: prob = 0.5
classifer: minScore = 0.45  doffset = 0.5 dStart = NA
method = mutinfo  D = 0.21 pmmi = 0.120 
matches: 470, 471
      below above score match  min median  max
471       5     0  0.91     1 0.09   0.12 0.16
470       4     0  0.89     1 0.04   0.07 0.10
294       0     5  0.00     0 0.42   0.47 0.51
303       0     5  0.00     0 0.45   0.47 0.54
47880     0     5  0.00     0 0.46   0.47 0.50
70775     0     5  0.00     0 0.46   0.47 0.50

--------------- rank species_subgroup (depth 1) --------------------
thresh: prob = 
classifer: minScore = 0.45  doffset = 0.5 dStart = 0.09
method = user  D = 0.09 pmmi =  
matches: 
       below above score match min median  max
578833     0     5     0     0 0.5   0.52 0.54

--------------- rank species_group (depth 1) --------------------
thresh: prob = 0.5
classifer: minScore = 0.45  doffset = 0.5 dStart = NA
method = mutinfo  D = 0.29 pmmi = 0.287 
matches: 
       below above score match  min median  max
136843     0     5     0     0 0.42   0.47 0.51
136845     0    30     0     0 0.45   0.48 0.62
136846     0     5     0     0 0.50   0.52 0.54
136841     0     5     0     0 0.57   0.59 0.62
655183     0     5     0     0 1.50   1.51 1.51
671232     0    10     0     0 1.62   1.66 1.71

--------------- rank genus (depth 2) --------------------
thresh: prob = 0.5
classifer: minScore = 0.45  doffset = 0.5 dStart = NA
method = mutinfo  D = 0.33 pmmi = 0.845 
matches: 469
    below above score match  min median  max
469     9     0  0.95     1 0.04    0.1 0.16
286     0    45  0.00     0 0.42    0.5 0.62
----------------------------------------------

============================================================
 matches: Acinetobacter
============================================================

--------------- rank species (depth 2) --------------------
thresh: prob = 0.5
classifer: minScore = 0.45  doffset = 0.5 dStart = NA
method = mutinfo  D = 0.21 pmmi = 0.120 
matches: Acinetobacter baumannii, Acinetobacter calcoaceticus
                            below above score match  min median  max
Acinetobacter calcoaceticus     5     0  0.91     1 0.09   0.12 0.16
Acinetobacter baumannii         4     0  0.89     1 0.04   0.07 0.10
Pseudomonas fluorescens         0     5  0.00     0 0.42   0.47 0.51
Pseudomonas putida              0     5  0.00     0 0.45   0.47 0.54
Pseudomonas fulva               0     5  0.00     0 0.46   0.47 0.50
Pseudomonas plecoglossicida     0     5  0.00     0 0.46   0.47 0.50

--------------- rank species_subgroup (depth 1) --------------------
thresh: prob = 
classifer: minScore = 0.45  doffset = 0.5 dStart = 0.09
method = user  D = 0.09 pmmi =  
matches: 
                              below above score match min median  max
Pseudomonas stutzeri subgroup     0     5     0     0 0.5   0.52 0.54

--------------- rank species_group (depth 1) --------------------
thresh: prob = 0.5
classifer: minScore = 0.45  doffset = 0.5 dStart = NA
method = mutinfo  D = 0.29 pmmi = 0.287 
matches: 
                              below above score match  min median  max
Pseudomonas fluorescens group     0     5     0     0 0.42   0.47 0.51
Pseudomonas putida group          0    30     0     0 0.45   0.48 0.62
Pseudomonas stutzeri group        0     5     0     0 0.50   0.52 0.54
Pseudomonas aeruginosa group      0     5     0     0 0.57   0.59 0.62
Lactobacillus casei group         0     5     0     0 1.50   1.51 1.51
Streptococcus anginosus group     0    10     0     0 1.62   1.66 1.71

--------------- rank genus (depth 2) --------------------
thresh: prob = 0.5
classifer: minScore = 0.45  doffset = 0.5 dStart = NA
method = mutinfo  D = 0.33 pmmi = 0.845 
matches: Acinetobacter
              below above score match  min median  max
Acinetobacter     9     0  0.95     1 0.04    0.1 0.16
Pseudomonas       0    45  0.00     0 0.42    0.5 0.62
----------------------------------------------
[1] "unit_output/test_bvseqs03.pdf"
Timing stopped at: 0.568 0.004 0.575
Error in xyplot(x ˜ y, data = data.frame(x = 1:10, y = 1:10)) : 
  could not find function "xyplot"
 done successfully.



Executing test function test_strep01  ... 
   classify   (depth 1):
   classifier (depth 1): 149 elements in reference set
   classifier (depth 1): running findThreshold, method="mutinfo"
   findThreshold (depth 1): (in): method = mutinfo
   findThreshold (depth 1): (in): within: 463   between: 10563
   findThreshold (depth 1): (out): D = 1.17 pmmi = 0.20
   classifier (depth 1): bkpt = 1.175
   classifier (depth 1): matches include S mitis, S pneumoniae, S pseudopneumoniae
   classify   (depth 1): threshIsValid: TRUE 
   classify   (depth 1): moreThanOneMatch: TRUE 
   classify   (depth 1): remainingGroupsLargeEnough: TRUE 
   classify   (depth 1): remainingNotAllMatches: TRUE 
   classify   (depth 1): running classify from depth 1
      classify   (depth 2):
      classifier (depth 2): 14 elements in reference set
      classifier (depth 2): running findThreshold, method="mutinfo"
      findThreshold (depth 2): (in): method = mutinfo
      findThreshold (depth 2): (in): within: 42   between: 49
      findThreshold (depth 2): (out): D = 0.46 pmmi = 0.30
      classifier (depth 2): bkpt = 0.460
      classifier (depth 2): matches include S mitis, S pseudopneumoniae
      classify   (depth 2): threshIsValid: TRUE 
      classify   (depth 2): moreThanOneMatch: TRUE 
      classify   (depth 2): remainingGroupsLargeEnough: TRUE 
      classify   (depth 2): remainingNotAllMatches: TRUE 
      classify   (depth 2): running classify from depth 2
         classify   (depth 3):
         classifier (depth 3): 10 elements in reference set
         classifier (depth 3): running findThreshold, method="mutinfo"
         findThreshold (depth 3): (in): method = mutinfo
         findThreshold (depth 3): (in): within: 36   between: 9
         findThreshold (depth 3): (out): D = NA pmmi = -0.05
         classifier (depth 3): bkpt = NA
         classifier (depth 3): matches include 
         classify   (depth 3): threshIsValid: FALSE 
         classify   (depth 3): moreThanOneMatch: FALSE 
         classify   (depth 3): remainingGroupsLargeEnough: FALSE 
         classify   (depth 3): remainingNotAllMatches: TRUE 
         classify   (depth 3): stopping at depth 3
         classify   (depth 3): no matches on final iteration, returning previous result
[1] "unit_output/test_strep01.pdf"
 done successfully.



Executing test function test_actino  ...  done successfully.



Executing test function test_bvseqs  ...  done successfully.



Executing test function test_strep  ...  done successfully.



Executing test function test_ROC  ... Timing stopped at: 0.004 0 0.011
Error in package.version("ROC") : 
  could not find function "package.version"
 done successfully.



Executing test function test_findPMMI_strep01  ...  done successfully.



Executing test function test_findPMMI_strep02  ...  done successfully.



Executing test function test_findThreshold_strep01  ...  done successfully.



Executing test function test_getThresh_01  ...  done successfully.



Executing test function test_getThresh_02  ...  done successfully.



Executing test function test_plotDistances_strep01  ... [1] "unit_output/test_plotDistances_strep01.pdf"
 done successfully.



Executing test function test_plotDistances_strep02  ... [1] "unit_output/test_plotDistances_strep02.pdf"
 done successfully.



Executing test function test_plotMutinfo_strep01  ... [1] "unit_output/test_plotMutinfo_strep01.pdf"
 done successfully.



Executing test function test_partition_01  ...  done successfully.



Executing test function test_bvseqs01  ... 
============================================================
 matches: 469
============================================================

--------------- rank species (depth 1) --------------------
thresh: prob = 0.5
classifer: minScore = 0.45  doffset = 0.5 dStart = NA
method = mutinfo  D = 0.09 pmmi = 0.049 
matches: 
      below above score match  min median  max
470       2     2  0.44     0 0.04   0.07 0.10
471       1     4  0.18     0 0.09   0.12 0.16
294       0     5  0.00     0 0.42   0.47 0.51
303       0     5  0.00     0 0.45   0.47 0.54
47880     0     5  0.00     0 0.46   0.47 0.50
70775     0     5  0.00     0 0.46   0.47 0.50
76759     0     5  0.00     0 0.45   0.48 0.51
78327     0     5  0.00     0 0.46   0.48 0.54
(... plus 85 groups not shown)

--------------- rank species_subgroup (depth 1) --------------------
thresh: prob = 
classifer: minScore = 0.45  doffset = 0.5 dStart = 0.09
method = user  D = 0.09 pmmi =  
matches: 
       below above score match min median  max
578833     0     5     0     0 0.5   0.52 0.54

--------------- rank species_group (depth 1) --------------------
thresh: prob = 0.5
classifer: minScore = 0.45  doffset = 0.5 dStart = NA
method = mutinfo  D = 0.29 pmmi = 0.287 
matches: 
       below above score match  min median  max
136843     0     5     0     0 0.42   0.47 0.51
136845     0    30     0     0 0.45   0.48 0.62
136846     0     5     0     0 0.50   0.52 0.54
136841     0     5     0     0 0.57   0.59 0.62
655183     0     5     0     0 1.50   1.51 1.51
671232     0    10     0     0 1.62   1.66 1.71

--------------- rank genus (depth 2) --------------------
thresh: prob = 0.5
classifer: minScore = 0.45  doffset = 0.5 dStart = NA
method = mutinfo  D = 0.33 pmmi = 0.845 
matches: 469
    below above score match  min median  max
469     9     0  0.95     1 0.04    0.1 0.16
286     0    45  0.00     0 0.42    0.5 0.62
----------------------------------------------

============================================================
 matches: Acinetobacter
============================================================

--------------- rank species (depth 1) --------------------
thresh: prob = 0.5
classifer: minScore = 0.45  doffset = 0.5 dStart = NA
method = mutinfo  D = 0.09 pmmi = 0.049 
matches: 
                            below above score match  min median  max
Acinetobacter baumannii         2     2  0.44     0 0.04   0.07 0.10
Acinetobacter calcoaceticus     1     4  0.18     0 0.09   0.12 0.16
Pseudomonas fluorescens         0     5  0.00     0 0.42   0.47 0.51
Pseudomonas putida              0     5  0.00     0 0.45   0.47 0.54
Pseudomonas fulva               0     5  0.00     0 0.46   0.47 0.50
Pseudomonas plecoglossicida     0     5  0.00     0 0.46   0.47 0.50
Pseudomonas monteilii           0     5  0.00     0 0.45   0.48 0.51
Pseudomonas mosselii            0     5  0.00     0 0.46   0.48 0.54
(... plus 85 groups not shown)

--------------- rank species_subgroup (depth 1) --------------------
thresh: prob = 
classifer: minScore = 0.45  doffset = 0.5 dStart = 0.09
method = user  D = 0.09 pmmi =  
matches: 
                              below above score match min median  max
Pseudomonas stutzeri subgroup     0     5     0     0 0.5   0.52 0.54

--------------- rank species_group (depth 1) --------------------
thresh: prob = 0.5
classifer: minScore = 0.45  doffset = 0.5 dStart = NA
method = mutinfo  D = 0.29 pmmi = 0.287 
matches: 
                              below above score match  min median  max
Pseudomonas fluorescens group     0     5     0     0 0.42   0.47 0.51
Pseudomonas putida group          0    30     0     0 0.45   0.48 0.62
Pseudomonas stutzeri group        0     5     0     0 0.50   0.52 0.54
Pseudomonas aeruginosa group      0     5     0     0 0.57   0.59 0.62
Lactobacillus casei group         0     5     0     0 1.50   1.51 1.51
Streptococcus anginosus group     0    10     0     0 1.62   1.66 1.71

--------------- rank genus (depth 2) --------------------
thresh: prob = 0.5
classifer: minScore = 0.45  doffset = 0.5 dStart = NA
method = mutinfo  D = 0.33 pmmi = 0.845 
matches: Acinetobacter
              below above score match  min median  max
Acinetobacter     9     0  0.95     1 0.04    0.1 0.16
Pseudomonas       0    45  0.00     0 0.42    0.5 0.62
----------------------------------------------

============================================================
 matches: Acinetobacter
============================================================

--------------- rank species (depth 1) --------------------
thresh: prob = 0.5
classifer: minScore = 0.45  doffset = 0.5 dStart = NA
method = mutinfo  D = 0.09 pmmi = 0.049 
matches: 
                 below above score match  min median  max
Ac...r baumannii     2     2  0.44     0 0.04   0.07 0.10
Ac...lcoaceticus     1     4  0.18     0 0.09   0.12 0.16
Ps...fluorescens     0     5  0.00     0 0.42   0.47 0.51
Ps...onas putida     0     5  0.00     0 0.45   0.47 0.54
Ps...monas fulva     0     5  0.00     0 0.46   0.47 0.50
Ps...oglossicida     0     5  0.00     0 0.46   0.47 0.50
Ps...s monteilii     0     5  0.00     0 0.45   0.48 0.51
Ps...as mosselii     0     5  0.00     0 0.46   0.48 0.54
(... plus 85 groups not shown)

--------------- rank species_subgroup (depth 1) --------------------
thresh: prob = 
classifer: minScore = 0.45  doffset = 0.5 dStart = 0.09
method = user  D = 0.09 pmmi =  
matches: 
                 below above score match min median  max
Ps...ri subgroup     0     5     0     0 0.5   0.52 0.54

--------------- rank species_group (depth 1) --------------------
thresh: prob = 0.5
classifer: minScore = 0.45  doffset = 0.5 dStart = NA
method = mutinfo  D = 0.29 pmmi = 0.287 
matches: 
                 below above score match  min median  max
Ps...scens group     0     5     0     0 0.42   0.47 0.51
Ps...utida group     0    30     0     0 0.45   0.48 0.62
Ps...tzeri group     0     5     0     0 0.50   0.52 0.54
Ps...inosa group     0     5     0     0 0.57   0.59 0.62
La...casei group     0     5     0     0 1.50   1.51 1.51
St...nosus group     0    10     0     0 1.62   1.66 1.71

--------------- rank genus (depth 2) --------------------
thresh: prob = 0.5
classifer: minScore = 0.45  doffset = 0.5 dStart = NA
method = mutinfo  D = 0.33 pmmi = 0.845 
matches: Acinetobacter
              below above score match  min median  max
Acinetobacter     9     0  0.95     1 0.04    0.1 0.16
Pseudomonas       0    45  0.00     0 0.42    0.5 0.62
----------------------------------------------
 done successfully.



Executing test function test_strep01  ... 
============================================================
 matches: S mitis, S pseudopneumoniae
============================================================

--------------- rank  (depth 1) --------------------
thresh: prob = 0.5
classifer: minScore = 0.45  doffset = 0.5 dStart = NA
method = mutinfo  D = 1.17 pmmi = 0.199 
matches: S mitis, S pneumoniae, S pseudopneumoniae
                   below above score match  min median  max
S mitis                9     0  0.95     1 0.00   0.38 0.58
S pneumoniae           4     0  0.89     1 0.56   0.60 0.97
S pseudopneumoniae     1     0  0.67     1 0.39   0.39 0.39
S australis            0     1  0.00     0 2.00   2.00 2.00
S infantis             0     2  0.00     0 2.23   2.42 2.61
S peroris              0     1  0.00     0 2.43   2.43 2.43
S sanguinis            0     5  0.00     0 3.74   4.04 5.73
S cristatus            0     1  0.00     0 4.61   4.61 4.61
(... plus 42 groups not shown)

--------------- rank  (depth 2) --------------------
thresh: prob = 0.5
classifer: minScore = 0.45  doffset = 0.5 dStart = NA
method = mutinfo  D = 0.46 pmmi = 0.300 
matches: S mitis, S pseudopneumoniae
                   below above score match  min median  max
S mitis                7     2  0.74     1 0.00   0.38 0.58
S pseudopneumoniae     1     0  0.67     1 0.39   0.39 0.39
S pneumoniae           0     4  0.00     0 0.56   0.60 0.97
----------------------------------------------
 done successfully.

> 
> printTextProtocol(testData, showDetails=TRUE)
RUNIT TEST PROTOCOL -- Wed Apr 11 22:19:59 2018 
*********************************************** 
Number of test functions: 22 
Number of errors: 3 
Number of failures: 0 

 
1 Test Suite : 
allSuite - 22 test functions, 3 errors, 0 failures
ERROR in test_bvseqs01: Error in xyplot(x ˜ y, data = data.frame(x = 1:10, y = 1:10)) : 
  could not find function "xyplot"
ERROR in test_bvseqs03: Error in xyplot(x ˜ y, data = data.frame(x = 1:10, y = 1:10)) : 
  could not find function "xyplot"
ERROR in test_ROC: Error in package.version("ROC") : 
  could not find function "package.version"



Details 
*************************** 
Test Suite: allSuite 
Test function regexp: ^test.+ 
Test file regexp: .*_test\.R$ 
Involved directory: 
unit 
--------------------------- 
Test file: unit/classifier_test.R 
test_strep01: (3 checks) ... OK (0.05 seconds)
test_strep02: (3 checks) ... OK (0.2 seconds)
test_strep03: (3 checks) ... OK (0.02 seconds)
--------------------------- 
Test file: unit/classifyIter_test.R 
test_bvseqs01: ERROR !! 
Error in xyplot(x ˜ y, data = data.frame(x = 1:10, y = 1:10)) : 
  could not find function "xyplot"
test_bvseqs02: (0 checks) ... OK (0.3 seconds)
test_bvseqs03: ERROR !! 
Error in xyplot(x ˜ y, data = data.frame(x = 1:10, y = 1:10)) : 
  could not find function "xyplot"
--------------------------- 
Test file: unit/classify_test.R 
test_strep01: (0 checks) ... OK (0.29 seconds)
--------------------------- 
Test file: unit/data_test.R 
test_actino: (2 checks) ... OK (0.01 seconds)
test_bvseqs: (2 checks) ... OK (0.02 seconds)
test_strep: (2 checks) ... OK (0.01 seconds)
--------------------------- 
Test file: unit/dependencies_test.R 
test_ROC: ERROR !! 
Error in package.version("ROC") : 
  could not find function "package.version"
--------------------------- 
Test file: unit/findThreshold_test.R 
test_findPMMI_strep01: (0 checks) ... OK (0.03 seconds)
test_findPMMI_strep02: (0 checks) ... OK (0.03 seconds)
test_findThreshold_strep01: (1 checks) ... OK (0.04 seconds)
test_getThresh_01: (2 checks) ... OK (0 seconds)
test_getThresh_02: (4 checks) ... OK (0 seconds)
test_plotDistances_strep01: (0 checks) ... OK (0.06 seconds)
test_plotDistances_strep02: (0 checks) ... OK (0.16 seconds)
test_plotMutinfo_strep01: (0 checks) ... OK (0.14 seconds)
--------------------------- 
Test file: unit/partition_test.R 
test_partition_01: (2 checks) ... OK (0.02 seconds)
--------------------------- 
Test file: unit/print_test.R 
test_bvseqs01: (0 checks) ... OK (0.39 seconds)
test_strep01: (0 checks) ... OK (0.05 seconds)
> 
> #q(runLast=FALSE)
> 
> proc.time()
   user  system elapsed 
  4.876   0.072   4.955 

name	user	system	elapsed
actino	0.012	0.004	0.016
bvseqs	0.000	0.000	0.002
classify	0.480	0.016	0.506
clst-package	0.088	0.000	0.089
findThreshold	0.040	0.000	0.038
plotDistances	0.188	0.000	0.189
printClst	0.004	0.000	0.003
scaleDistPlot	5.692	0.020	5.714
strep	0.000	0.000	0.001